Question: How to get hold of the gff files for RepeatMAsker annotated human genome
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gravatar for kwicher
3 months ago by
kwicher10
kwicher10 wrote:

Hello

How to get hold of the precomputed RepeatMasker gff files for human genome?

Thanks

K

human repaetmasker gff genome • 178 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by kwicher10

http://www.repeatmasker.org/species/hg.html

With that : https://github.com/vikas0633/perl/blob/master/cnv_repmask2gff.pl

ADD REPLYlink modified 3 months ago • written 3 months ago by Bastien Hervé4.4k

Thank you.

Just a comment. It spit out the following message at the beginning: Use of uninitialized value $ENV{"DP_GFF"} in uc at cnv_repmask2gff.pl line 50.

Though seems to be doing what it is meant to.

ADD REPLYlink written 3 months ago by kwicher10
1

Please use the "add reply" gray button below a comment to add a comment to mine, this keeps the thread well indent

I guess it is no big deal, it does not find the env variable DP_GFF, which you do not need if you add this option to the command line :

--gff-ver GFF3
ADD REPLYlink modified 3 months ago • written 3 months ago by Bastien Hervé4.4k
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